Intro Puzzles
Here you can see the original instructions of the intro puzzles. Translations: Deutsch | Svenska Tip : read carefully the texts, press on button "tell me more", reset the puzzle after a few try and redo. Sidechains Level 1-1: One Small Clash This is a protein. We need your help to fold it into the right shape! You can drag SIDECHAINS with the mouse. Get rid of the clash by clicking and dragging one of the sidechains away from the other. Level 1-2: Swing It Around You can't see the sidechains from this angle! Click and drag on the white background to rotate the view. You can also move or zoom by holding ctrl or shift while you drag. Level 1-3: Hide the Hydrophobic The big hydrophobic sidechain is out in the open! Orange sidechains are HYDROPHOBIC. They want to be buried inside the protein. EXPOSEDS may appear on unburied hydrophobics! (yellow ball moving) Blue sidechains need plenty of space. They should point outward. Orange sidechains should be kept surrounded. Hide it in the empty space in the protein's interior and move the blue hydrophilic away outside. tip : move the orange sidechain in the center. Level 1-4: Shake It Off Orange together, blue apart. You can zoom in and out. Hold shift and drag the background. The backbone is red with clashes! Make it green. You've earned a new tool! SHAKE moves all the sidechains at once. It will find a good spot for each of them. Shake It Off Stop the Shake by pressing the space bar Photos of the solutions and some intermediate steps: ' One Small Clash.png Swing It Around 1.png Swing It Around 2.png Shake It Off 1.png Shake It Off 2.png ' Backbone packing Level 2-1: When Backbones Collide This clash can't be fixed moving sidechains alone! Click and drag on the big backbone to pull it. Level 2-2: Close the Gap This protein needs to be folded back together! Bring the two halves close so the hydrophobics match up. Then try a Wiggle Backbone to let the backbone slowly relax into a better shape. Try to get close to this guide. (the shadow) Oops, the protein is too far apart. Want to reset? You've earned a new tool! You can now WIGGLE the backbone. Use it to relax the protein after pulling. Wiggle settles the backbone into a more natural shape. You can stop it by pressing the space bar. tip : move the sheet on the shadow, take care that the orange sidechains (hydrophobics) are inside the sandwitch. Level 2-3: Twin Pack The curly helices are too far apart! Pack the helices closely, so the hydrophobics are squished between them. Then Shake and Wiggle! You're close to the guide! Even if your score went down, try a Shake then Wiggle combination to get more points! Level 2-4: Triple Packed The hydrophobics in the center are exposed! You can Freeze parts of the protein to hold them in place while you pull. Just hold shift and double click the area you want to Freeze. As many have problems with this one, here is LennStar's guide, proofed to be working several times: If you have done anythink, restart the puzzle. (best from puzzle menu if you have rotated the view) Now, as the puzzle is fresh, do it this way: Take the lonely upper helix at the point where the arrow from the hint is pointing. Now move the mouse down-left to the red balls. (the voids, if you don't see them, either activate them in the views options, or target the one red hydrophobic in the foreground) If a clash appears, pull a little bit more and stop. Now shake and wiggle. That should do the trick. Congratulations! Hydrogen Bonding Level 3-1: Sheets Together This protein is made of two flat sheets. Pull those sheets together! They like that. Level 3-2: Lonely Sheets Two little sheets, lost and alone... Help them find each other with a Rubber Band: hold down shift while you click on one sheet and drag to the other. Wiggle to start them moving. Level 3-3: Sheets and Ladders Three sheets have been torn apart! Rubber Band them together with a shift click drag. Once they are close enough, you can remove the bands and Wiggle again. Level 3-4: Lock and Lower One of the sheets is out of place! Rubber bands can keep the sheets connected. Remember you can also shift click to Freeze, and Shake and Wiggle once they are close enough. Level 4-1: Basic Threading This level will intriduce the powerful Alignment tool. It will let you use the structure of real proteins, called TEMPLATES, by THREADING. Click on the smiley button. This 3D strcutures shows the backbone of the template. (ball and sticks) The bottom row of the letters is the TEMPLATE SEQUENCE. you can see it in 3D as spheres connected by lines. The top row of letters is the sequance of your protein. The cylinders in 3D show how its backbones lines up with the template. When you THREAD, your protein will try to fit onto the 3D template where the cylinders are. Click the little smiley to try threading. Level 4-4: Rebuild Repairs The red loop is stuck in the wrong shape! Try using the Rebuild tool to open up that loop. You'll see it when you ctrl click on the loop. You've started to Rebuild the backbone! The protein will try out some different shapes. Once it looks good enough, click Stop Rebuild and try a Shake and Wiggle to get rid of clashes. Tweak and Rebuild Level 5-1: Turn It Down The helix has turned and exposed a hydrophobic! Rotate it back into place with the Tweak tool. You'll see it when you ctrl click on the helix. You've started a Tweak! Click and hold on the purple arrows to rotate the protein in the direction you want it to go. Watch your score! If you turn it too far, you can try turning it back or just Undo. Level 5-2: The Right Rotation Find the one helix that needs rotating and fix it with the Tweak tool! Look for a hydrophobic sticking out in the open, and turn it back in. You can always Undo. Level 5-3: Flippin' Sheets One of the sheets is twisted the wrong way! Look for the sheet with the exposed hydrophobics, and click the new straight arrows on the Tweak tool to shift and flip it. You've started a Tweak! Click and hold on the curved purple arrows to rotate the protein in the direction you want it to go or use the straight purple arrows to shift and flip the sheet in that direction. Watch your score! If you turn it too far, you can try turning it back or just Undo. LennStar's guide: This is one puzzle that really dislikes being mishandled. It took me at least 5 tries. This is how to do it: If you already have done anything to it, reset the puzzle. (Hint: You propably have to move the 4 sheets to the foreground, the one with the arrow pointing on with the short end to the left. You can also go back to puzzle menu to get the right view.) Now right click on the one sheet where the arrow from the text points to. Click tweak. Now click one time on the straight arrow to the right. Now the sheet should flip. use shake and wiggle it. That should raise your score to the needed points. Level 5-4: Rubber Band Reversal A hydrophobic is flipped the wrong way! Reverse the zig zag with two Rubber Bands and a Rebuild: one band to bring the hydrophobic down, and another to bring the hydrophilic up. You can attach a Rubber Band to empty space! Level 5-5: Moving along Sometimes you can move whole piece of the protein.Click on a piece to bring on up the move tool. Then press and hold down RIGHT BUTTON anaywhere on the tool to drag the piece around. Tip : Click on the helix, then on the purple star with the right button, then move the helix on the shadow, rotate the view to check then shake and wiggle. Protein Design Level 6-1: Intro to Design Learn to change the side chains using the Design Mode tool. Level 6-2: Swapping Side Chains Change some more sidechains using the Design Mode tool. Level 6-3: Mass Mutate Change some sidechains by hand using the Design Mode tool. When you have change enough sidechains, you will be introduced to the Mutate command. Level 6-4: Insertion and Deletion ''' In Design Mode you can right click on the backbone and change the length of the backbone. '''Level 7-3: DNA Pairing Use Design Mode to find the correct match for the incorrectly paired sidechains. DNA sidechains pair according to color and size. Match sidechains of same color and opposite sizes to make lots of bonds! Level 7-4: DNA and Protein DNA can hydrogen bond to protein. Mutate the proteins to form better bonds.